PhD Chapter 1
Campaign 2016 - Maps and exploration
This series of files compile analyses done for the specific analysis of Chapter 1, for the regional campaign of 2016.
All analyses have been done with PRIMER-e 6 and R 4.0.2.
Click on the table of contents in the left margin to assess a specific analysis.
Click on a figure to zoom it
We used data from subtidal ecosystems (see metadata files for more information). Only stations that have been sampled both for abiotic parameters and benthic species were included.
Selected variables for the analyses:
- Depth of the station: depth (only for ANCOVAs)
- Percentage of organic matter: om
- Percentage of gravel: gravel
- Percentage of sand: sand
- Percentage of silt: silt
- Percentage of clay: clay
- Concentration of arsenic: arsenic
- Concentration of cadmium: cadmium
- Concentration of chromium: chromium
- Concentration of copper: copper
- Concentration of iron: iron
- Concentration of manganese: manganese
- Concentration of mercury: mercury
- Concentration of lead: lead
- Concentration of zinc: zinc
- Specific richness: S
- Total density of individuals: N
- Shannon’s diversity: H
- Piélou’s evenness: J
Abundances of Mesodesma arctatum (Marc) and Cistenides granulata (Cgra) were also considered (see IndVal and SIMPER results).
As data is missing for metal concentrations outside BSI, two Designs have been used:
- Design 1: stations at BSI, CPC, BDA, MR with habitat parameters
- Design 2: stations at BSI with heavy metal concentrations.
Statistics for each variable considered:
| Mean | SD | SE | Median | Min | Max | 95% CI | |
|---|---|---|---|---|---|---|---|
| depth | 20.235 | 16.929 | 2.582 | 17.600 | 1.000 | 65.900 | 5.060 |
| om | 0.856 | 0.891 | 0.136 | 0.491 | 0.209 | 3.863 | 0.266 |
| gravel | 0.043 | 0.092 | 0.014 | 0.000 | 0.000 | 0.359 | 0.028 |
| sand | 0.612 | 0.381 | 0.058 | 0.702 | 0.000 | 1.001 | 0.114 |
| silt | 0.285 | 0.328 | 0.050 | 0.116 | 0.000 | 0.942 | 0.098 |
| clay | 0.060 | 0.106 | 0.016 | 0.016 | 0.000 | 0.415 | 0.032 |
| S | 4.930 | 3.135 | 0.478 | 4.000 | 0.000 | 13.000 | 0.937 |
| N | 18.977 | 24.421 | 3.724 | 12.000 | 0.000 | 140.000 | 7.299 |
| H | 1.124 | 0.613 | 0.093 | 1.213 | 0.000 | 2.307 | 0.183 |
| J | 0.744 | 0.291 | 0.044 | 0.835 | 0.000 | 1.000 | 0.087 |
| arsenic | 4.300 | 4.759 | 0.971 | 2.500 | 0.800 | 21.300 | 1.904 |
| cadmium | 0.153 | 0.048 | 0.010 | 0.145 | 0.080 | 0.270 | 0.019 |
| chromium | 49.667 | 24.539 | 5.009 | 40.500 | 17.000 | 111.000 | 9.817 |
| copper | 9.787 | 7.764 | 1.585 | 7.800 | 2.400 | 28.800 | 3.106 |
| iron | 45356.633 | 17343.813 | 3540.291 | 39733.450 | 21938.100 | 85408.600 | 6938.843 |
| manganese | 776.662 | 362.884 | 74.073 | 677.850 | 318.400 | 1657.100 | 145.181 |
| mercury | 0.023 | 0.017 | 0.004 | 0.019 | 0.007 | 0.091 | 0.007 |
| lead | 5.421 | 3.021 | 0.617 | 4.650 | 1.900 | 12.200 | 1.209 |
| zinc | 59.358 | 30.340 | 6.193 | 47.700 | 26.900 | 141.400 | 12.138 |
| Mean | SD | SE | Median | Min | Max | 95% CI | |
|---|---|---|---|---|---|---|---|
| depth | 20.527 | 17.297 | 3.011 | 15.300 | 3.400 | 61.900 | 5.901 |
| om | 0.476 | 0.389 | 0.068 | 0.315 | 0.168 | 1.597 | 0.133 |
| gravel | 0.049 | 0.147 | 0.026 | 0.000 | 0.000 | 0.809 | 0.050 |
| sand | 0.832 | 0.270 | 0.047 | 0.960 | 0.000 | 1.000 | 0.092 |
| silt | 0.095 | 0.180 | 0.031 | 0.023 | 0.000 | 0.650 | 0.061 |
| clay | 0.024 | 0.086 | 0.015 | 0.005 | 0.000 | 0.497 | 0.029 |
| S | 4.333 | 2.558 | 0.445 | 4.000 | 1.000 | 9.000 | 0.873 |
| N | 19.970 | 27.779 | 4.836 | 12.000 | 2.000 | 142.000 | 9.478 |
| H | 0.975 | 0.589 | 0.102 | 0.974 | 0.000 | 1.985 | 0.201 |
| J | 0.690 | 0.302 | 0.053 | 0.840 | 0.000 | 1.000 | 0.103 |
1. Maps
1.1. General map
1.2. Parameters maps
For maps of heavy metal concentrations, stations have been grouped based on Environment Canada (2007) classification of sediment toxicity (grey = low toxicity, red = high toxicity).
OM
Gravel
Sand
Silt
Clay
Arsenic
Cadmium
Chromium
Copper
Iron
Manganese
Mercury
Lead
Zinc
Species
Richness
Density
Diversity
Evenness
2. Figures
2.1. Barplots
Two types of barplots are available: one for the means by region, and one for the means by depth class. The latter have been done by classifying stations along three groups, based on their depth: shallow (0-10 m), medium (10-25 m) and deep (> 25 m). These thresholds are not supported by evidence, but allow to get a balanced design (26 stations for each depth class). However, we have been using PERMANOVA with depth as a covariate, instead of using these classes as a third factor.
Heavy metals are not presented here, as they were only sampled at BSI stations.
Regions
Organic matter
Grain-size
Species abundances
Diversity indices
Depth classes
Organic matter
Grain-size
Species abundances
Diversity indices
2.2. Phylum frequencies
Conditions
| Phylum | HI | R |
|---|---|---|
| Annelida | 275 | 231 |
| Echinodermata | 230 | 162 |
| Mollusca | 196 | 189 |
| Arthropoda | 110 | 73 |
| Platyhelminthes | 3 | 0 |
| Nematoda | 1 | 0 |
| Nemertea | 1 | 0 |
| Brachiopoda | 0 | 2 |
| Cnidaria | 0 | 2 |
Regions
| Phylum | BSI | CPC | BDA | MR |
|---|---|---|---|---|
| Annelida | 206 | 69 | 188 | 43 |
| Mollusca | 151 | 45 | 89 | 100 |
| Arthropoda | 97 | 13 | 30 | 43 |
| Echinodermata | 24 | 206 | 24 | 138 |
| Platyhelminthes | 3 | 0 | 0 | 0 |
| Nematoda | 1 | 0 | 0 | 0 |
| Nemertea | 1 | 0 | 0 | 0 |
| Brachiopoda | 0 | 0 | 0 | 2 |
| Cnidaria | 0 | 0 | 0 | 2 |
2.3. Species estimation curves
2.4. Principal Component Analysis
Design 1
Variables have been standardized by mean and standard-deviation.
Design 2
Variables have been standardized by mean and standard-deviation.
2.5. Non-metric Multidimensional Scaling
Design 1
Variables have been standardized by mean and standard-deviation.
Design 2
Variables have been standardized by mean and standard-deviation.
Species
Stations with no species were deleted from this analysis.
2.6. Hierarchical Agglomerative Clustering
Design 1
Variables have been standardized by mean and standard-deviation.
## 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63
## 1 2 2 2 2 2 2 2 2 2 3 3 2 3 2 1 3 2 2 2
## 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 82 83 86
## 2 2 2 2 2 2 2 1 1 1 1 2 1 2 2 2 3 3 3 2
## 87 88 90 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108
## 2 2 3 1 3 2 1 3 1 3 1 1 3 2 3 3 1 2 1 3
## 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124
## 2 1 3 1 2 2 2 3 3 3 2 2 1 2 3 3
Design 2
Variables have been standardized by mean and standard-deviation.
## 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120
## 1 2 1 1 3 3 3 1 3 3 3 3 3 3 3 2 2 2 2 3
## 121 122 123 124
## 3 3 3 2
Species
Stations with no species were deleted from this analysis.
## 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63
## 1 1 1 1 1 1 1 1 1 2 1 1 3 1 2 2 1 2 2 2
## 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 82 83 86 87
## 1 1 1 1 3 1 2 2 1 1 2 2 1 1 2 2 1 3 1 2
## 90 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110
## 1 2 3 3 1 1 3 1 3 3 1 1 1 1 1 1 1 1 1 1
## 111 112 113 114 115 116 117 118 119 120 121 122 123 124
## 1 3 1 3 1 1 1 1 1 2 1 3 1 1